Proteins

Question 1

Primary structure of a protein.

Answer 1

Composed of a chain of amino acids maintained by peptide bonds.

C-terminus is the start of the chain.

N-terminus is the end of the chain.

Question 2

Secondary structure of a protein

Answer 2

Composed of the primary folding of the polypeptide chain into an alpha helix or beta pleated sheet.

Maintained by hydrogen bonds.

Question 3

Alpha helix

Answer 3

• Composed of a polypeptide chain coiled into a helical structure
• Hydrogen bonds are formed between amine and carboxyl group 4 amino acids down.
• This causes an outward turn every 3.6 amino acids and the sidechains to face outward.

Question 4

Beta pleated sheet

Answer 4

• Polypeptide chain laterally packed into beta strands.
• Hydrogen bonds are formed between the amine and carboxyl group of neighboring amino acids.
• Causes the side chains of the amino acids to be above and below the beta sheets.
• The sheets can run anti-parallel or parallel.

Question 5

Non-essential vs essential amino acids

Answer 5

Non essential: amino acids that are made in the body or obtained from breaking down other amino acids.

Essential amino acids:
Amino acids that are not made in the body and so can only be obtained from food.

Question 6

Protein domain

Answer 6

Globular unit of a protein from the same polypeptide chain.

Each domain is separated by an inner chain of the same polypeptide chain.

Each domain has a specific DNA sequence that performs a certain function even though it is from the same polypeptide.

Question 7

Signaling sequence in proteins

Answer 7

A sequence of 15-60 amino acids located in the polypeptide chain that signals for where the protein should go after synthesis.

Question 8

Creutzfelat-Jakob disease

Answer 8

(Also known as mad cow disease)

• Neurodegenerative disease caused by mis-folding of prion proteins in the brain.
• This causes subacute spongiform encephalopathy

Question 9

How does CFTR mutation affect protein structure?

Answer 9

The deletion of phenylamine at amino acid 508 causes an impaired Cl- transporter.

Question 10

Structures found in the protein that is not an alpha helix of beta pleated sheet.

Answer 10

• Loops
• Barrel: Where the first and last part of the strand closes
• Random coils.

Question 11

R-group interactions

Answer 11

• In an aqueous environment:
  Hydrophilic parts of the protein are external and exposed to the environment.

Hydrophobic side chains are internal, does not interact.

- Interactions included:
Hydrogen bonds
Van der Waal forces
Electrostatic attractions
Covalent bonds, Disulphide bonds

Question 12

Assisted folding of proteins

Answer 12

• Certain proteins assist the folding of proteins are molecular chaperones:

Do so without altering the protein shape

Prevents protein aggregation and repairs incorrectly folded proteins.

Heat shocking proteins: Stabilises protein folding in response to elevated temperatures

Question 13

Quaternary structure of a protein

Answer 13

R-group interactions between more than one polypeptide chains to form sub-units.

Question 14

Disulphide bonds

Answer 14

Covalent bond formed between Sulphur atoms attached to a polypeptide.
Found in cysteine.

This is an oxidation reaction:
Causes proteins with this bond to be located extracellular as the cytosol has reducing conditions.

Question 15

Folding funnel

Answer 15

Idea that proteins will always fold into the configuration that gives then the lowest free energy.

Proteins will fold until entropy is very low, which allows a stable molecule so that the bonds do not move.

Question 16

How can protein activity be regulated.

Answer 16

Controlling the amount present:
Controlling the synthesis
Proteasomes
Controlling secretion

Controlling the activity of the protein:
Post-translational modification
Further interactions with other molecules: i.e cofactors

Question 17

Proteasome

Answer 17

Protein complex that degrades protein that is in excess or that has folded incorrectly.

Causes proteolysis, which breaks down the peptide bonds in proteins.